Bikersmurf- It seems I have a differnt style of manifolds than you have. My flange isnt as far down as yours are. My flange is right after it drops down and is horizontal, almost like the one on your passenger side but higher. And that is where it is hitting the box. I moved the engine forward about an inch from your measurements and up a little higher it seems and I think this is going to work. Now I just have to make motormounts and see how it all worksout.
Huroneymoose- This is my second FJ40, Ive been workign on them for 7 years so believe me ive had my ups and downs with them lol. My first one I did a frame off restoration and a 4" lift and 33s. This one im doing a lot more modifications too. Its always a fun project, It started off as just a little project that I was just gunna use to go out tot he woods, here I am almsot 2 years later and replaced all my body panels, new motor, still got to rebuild axles, and then who knows. one thing definetly leads to another lol